1
|
Sánchez‐González Á, Grenut P, Gil A. Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone. J Comput Chem 2022; 43:804-821. [PMID: 35297513 PMCID: PMC9313584 DOI: 10.1002/jcc.26836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/28/2022] [Indexed: 12/14/2022]
Abstract
The influence of hydrogen bonds in model intercalated systems between guanine-cytosine and adenine-thymine DNA base pairs (bps) was analyzed with the popular intercalator 1,10-phenanthroline (phen) and derivatives obtained by substitution with OH and NH2 groups in positions 4 and 7. Semiempirical and Density Functional Theory (DFT) methods were used both including dispersion effects: PM6-DH2, M06-2X and B3LYP-D3 along with the recently developed near linear-scaling coupled cluster method DLPNO-CCSD(T) for benchmark calculations. Our results given by QTAIM and non-covalent interaction analysis confirmed the existence of hydrogen bonds created by OH and NH2 . The trends in the energy decomposition analysis for the interaction energy, ΔEint , showed that the ΔEelstat contributions are equal or even a little bit higher than the values for ΔEdisp . Such important ΔEelstat attractive contribution comes mainly from the conventional hydrogen bonds formed by OH and NH2 functional groups with DNA not only with bps but specially with the sugar and phosphate backbone. This behavior is very different from that of phen and other classical intercalators that cannot form conventional hydrogen bonds, where the ΔEdisp is the most important attractive contribution to the ΔEint . The inclusion of explicit water molecules in molecular dynamics simulations showed, as a general trend, that the hydrogen bonds with the bps disappear during the simulations but those with the sugar and phosphate backbone remain in time, which highlights the important role of the sugar and phosphate backbone in the stabilization of these systems.
Collapse
Affiliation(s)
- Ángel Sánchez‐González
- BioISI—Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de CiênciasUniversidade de Lisboa, Campo GrandeLisbonPortugal
| | - Pierre Grenut
- BioISI—Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de CiênciasUniversidade de Lisboa, Campo GrandeLisbonPortugal
| | - Adrià Gil
- BioISI—Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de CiênciasUniversidade de Lisboa, Campo GrandeLisbonPortugal
- ARAID FoundationZaragozaSpain
- Departamento de Química InorgánicaInstituto de Síntesis Química y Catálisis Homogénea (ISQCH) CSIC‐Universidad de Zaragoza, c/ Pedro Cerbuna 12ZaragozaSpain
| |
Collapse
|
2
|
Esteves T, Ferreira FA, Mota AT, Sánchez-González Á, Gil A, Andrade KH, Afonso CAM, Ferreira FC. Greener Strategy for Lupanine Purification from Lupin Bean Wastewaters Using a Molecularly Imprinted Polymer. ACS APPLIED MATERIALS & INTERFACES 2022; 14:18910-18921. [PMID: 35420019 PMCID: PMC9773177 DOI: 10.1021/acsami.2c02053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Lupanine is an alkaloid used in the pharma industry as a building block or precursor in the synthesis of sparteine and also explored for drug synthesis in the pharma industry as a chiral selector. This alkaloid is found in lupin bean processing wastewaters originated from the debittering process to make these beans edible. In this work, a computational chemistry approach was taken to design molecularly imprinted polymers (MIPs) selecting itaconic acid, a biobased building block, as a functional monomer that can provide higher affinities for lupanine. MIP-1 was prepared using lupanine as the template, itaconic acid as a functional monomer, and ethylene glycol dimethacrylate as a cross-linker by bulk polymerization. Lupanine was concentrated from lupin bean wastewater by nanofiltration, extracted with ethyl acetate, and purified using the synthesized MIP. MIP-1 was able to selectively recognize lupanine and improve the purity of lupanine from 78 to 88%, with 82% recovery of the alkaloid. These results show the potential application of this strategy to render the industrial process more sustainable.
Collapse
Affiliation(s)
- Teresa Esteves
- iBB—Institute
for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
- . Phone: +351 218419167
| | - Flávio A. Ferreira
- iBB—Institute
for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
| | - Ana Teresa Mota
- iBB—Institute
for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
| | - Ángel Sánchez-González
- Centro
de Química e Bioquímica and BioISI—Biosystems
and Integrative Sciences Institute, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Adrià Gil
- Centro
de Química e Bioquímica and BioISI—Biosystems
and Integrative Sciences Institute, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Késsia H.
S. Andrade
- Research
Institute for Medicine (iMED, ULisboa); Faculty of Pharmacy, Universidade de Lisboa, Avenida Prof. Gama Pinto, Lisboa 1649-003, Portugal
| | - Carlos A. M. Afonso
- Research
Institute for Medicine (iMED, ULisboa); Faculty of Pharmacy, Universidade de Lisboa, Avenida Prof. Gama Pinto, Lisboa 1649-003, Portugal
| | - Frederico Castelo Ferreira
- iBB—Institute
for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
| |
Collapse
|
3
|
Sánchez-González Á, Castro TG, Melle-Franco M, Gil A. From groove binding to intercalation: unravelling the weak interactions and other factors modulating the modes of interaction between methylated phenanthroline-based drugs and duplex DNA. Phys Chem Chem Phys 2021; 23:26680-26695. [PMID: 34825685 DOI: 10.1039/d1cp04529f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Several antitumor drugs base their cytotoxicity on their capacity to intercalate between base pairs of DNA. Nevertheless, it has been established that the mechanism of intercalation of drugs in DNA starts with the prior groove binding mode of interaction of the drug with DNA. Sometimes, for some kind of flat small molecules, groove binding does not produce any cytotoxic effect and the fast transition of such flat small molecules to the cytotoxic intercalation mode is desirable. This is the case of methylated phenanthroline (phen) derivatives, where, changes in the substitution in the position and number of methyl groups determine their capability as cytotoxic compounds and, therefore, it is a way for the modulation of cytotoxic effects. In this work, we studied this modulation by means of the interaction of the [Pt(en)(phen)]2+ complex and several derivatives by methylation of phen in different number and position and the d(GTCGAC)2 DNA hexamer via groove binding using PM6-DH2 and DFT-D methods. The analysis of the geometries, electronic structure and energetics of the studied systems was compared to experimental works to gain insight into the relation structure-interaction for the studied systems with cytotoxicity. The trends are explained by means of the Non-Covalent Interaction (NCI) index, the Energy Decomposition Analysis (EDA) and solvation contributions. Our results are in agreement with the experiments, in which the methylation of position 4 of phen seems to favour the interaction via groove binding thus making the transition to the intercalation cytotoxic mode difficult. Looking at the NCI results, these interactions come not only from the CH/π and CH/n interactions of the methyl group in position 4 but also from the ethylenediamine (en) ligand, whose orientation in the Pt complex was found in such a way that it produces a high number of weak interactions with DNA, especially with the sugar and phosphate backbone.
Collapse
Affiliation(s)
- Ángel Sánchez-González
- Centro de Química e Bioquímica and BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande 1749-016, Lisboa, Portugal.
| | - Tarsila G Castro
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Manuel Melle-Franco
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Adrià Gil
- Centro de Química e Bioquímica and BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande 1749-016, Lisboa, Portugal. .,CIC nanoGUNE BRTA, Tolosa Hiribidea 76, E-20018 Donostia - San Sebastian, Euskadi, Spain
| |
Collapse
|
4
|
Sánchez-González Á, Bandeira NAG, Ortiz de Luzuriaga I, Martins FF, Elleuchi S, Jarraya K, Lanuza J, Lopez X, Calhorda MJ, Gil A. New Insights on the Interaction of Phenanthroline Based Ligands and Metal Complexes and Polyoxometalates with Duplex DNA and G-Quadruplexes. Molecules 2021; 26:4737. [PMID: 34443326 PMCID: PMC8397986 DOI: 10.3390/molecules26164737] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022] Open
Abstract
This work provides new insights from our team regarding advances in targeting canonical and non-canonical nucleic acid structures. This modality of medical treatment is used as a form of molecular medicine specifically against the growth of cancer cells. Nevertheless, because of increasing concerns about bacterial antibiotic resistance, this medical strategy is also being explored in this field. Up to three strategies for the use of DNA as target have been studied in our research lines during the last few years: (1) the intercalation of phenanthroline derivatives with duplex DNA; (2) the interaction of metal complexes containing phenanthroline with G-quadruplexes; and (3) the activity of Mo polyoxometalates and other Mo-oxo species as artificial phosphoesterases to catalyze the hydrolysis of phosphoester bonds in DNA. We demonstrate some promising computational results concerning the favorable interaction of these small molecules with DNA that could correspond to cytotoxic effects against tumoral cells and microorganisms. Therefore, our results open the door for the pharmaceutical and medical applications of the compounds we propose.
Collapse
Affiliation(s)
- Ángel Sánchez-González
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Nuno A. G. Bandeira
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Iker Ortiz de Luzuriaga
- CIC nanoGUNE BRTA, Tolosa Hiribidea 76, Euskadi, 20018 Donostia-San Sebastián, Spain;
- Polimero eta Material Aurreratuak, Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain; (J.L.); (X.L.)
| | - Frederico F. Martins
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Sawssen Elleuchi
- Laboratoire de Chimie Inorganique, LR17ES07, Faculté de Sciences de Sfax, Université de Sfax, Sfax 3000, Tunisia; (S.E.); (K.J.)
| | - Khaled Jarraya
- Laboratoire de Chimie Inorganique, LR17ES07, Faculté de Sciences de Sfax, Université de Sfax, Sfax 3000, Tunisia; (S.E.); (K.J.)
| | - Jose Lanuza
- Polimero eta Material Aurreratuak, Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain; (J.L.); (X.L.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Xabier Lopez
- Polimero eta Material Aurreratuak, Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain; (J.L.); (X.L.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Maria José Calhorda
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Adrià Gil
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
- CIC nanoGUNE BRTA, Tolosa Hiribidea 76, Euskadi, 20018 Donostia-San Sebastián, Spain;
| |
Collapse
|
5
|
Ogawa N, Nagase H, Matsumoto T, Kaga M, Ishihara S, Endo T, Yasunaga T, Kawashima Y, Ueda H, Yamamoto H. Crystallographic evaluation of the conformation of quetiapine included in β-cyclodextrin. Int J Pharm 2020; 587:119625. [DOI: 10.1016/j.ijpharm.2020.119625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 10/23/2022]
|
6
|
Elleuchi S, Ortiz de Luzuriaga I, Sanchez-Gonzalez Á, Lopez X, Jarraya K, Calhorda MJ, Gil A. Computational Studies on the Binding Preferences of Molybdenum(II) Phenanthroline Complexes with Duplex DNA. The Important Role of the Ancillary Ligands. Inorg Chem 2020; 59:12711-12721. [DOI: 10.1021/acs.inorgchem.0c01793] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Sawssen Elleuchi
- Laboratoire de Chimie Inorganique, LR17ES07, Université de Sfax, Faculté de Sciences de Sfax, Route de Soukra Km 3.5, BP 1171, 3000 Sfax, Tunisia
| | - Iker Ortiz de Luzuriaga
- CIC nanoGUNE BRTA, Tolosa Hiribidea 76, E-20018 Donostia, San Sebastián, Euskadi, Spain
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, P.K. 107, 20018 Donostia, San Sebastián, Euskadi, Spain
| | - Ángel Sanchez-Gonzalez
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
| | - Xabier Lopez
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, P.K. 107, 20018 Donostia, San Sebastián, Euskadi, Spain
- Donostia International Physics Center, P.K. 1072, 20080 Donostia, San Sebastián, Euskadi, Spain
| | - Khaled Jarraya
- Laboratoire de Chimie Inorganique, LR17ES07, Université de Sfax, Faculté de Sciences de Sfax, Route de Soukra Km 3.5, BP 1171, 3000 Sfax, Tunisia
| | - Maria José Calhorda
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
| | - Adrià Gil
- CIC nanoGUNE BRTA, Tolosa Hiribidea 76, E-20018 Donostia, San Sebastián, Euskadi, Spain
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
| |
Collapse
|
7
|
Soliman SM, Albering JH, Sholkamy EN, El‐Faham A. Mono‐ and penta‐nuclear self‐assembled silver(I) complexes of pyrazolyl
s
‐triazine ligand; synthesis, structure and antimicrobial studies. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Saied M. Soliman
- Department of Chemistry, Faculty of ScienceAlexandria University PO Box 426, Ibrahimia Alexandria 21321 Egypt
| | - Jörg H. Albering
- Graz University of Technology Mandellstr. 11/III, A‐8010 Graz Austria
| | - Essam N. Sholkamy
- Department of Botany and MicrobiologyCollege of Science, King Saud University PO Box 2455 Riyadh 11451 Saudi Arabia
| | - Ayman El‐Faham
- Department of ChemistryCollege of Science, King Saud University PO Box 2455, Riyadh11451 Saudi Arabia
| |
Collapse
|
8
|
Bagheri S, Masoodi HR. The influence of CH … π interaction on coupling constants across N … H–F hydrogen bond in a substituted T-shaped configuration: a theoretical study. Mol Phys 2020. [DOI: 10.1080/00268976.2019.1580393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Sotoodeh Bagheri
- Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Hamid Reza Masoodi
- Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| |
Collapse
|
9
|
Affiliation(s)
- Rundong Zhao
- Materials and Energy Division, Beijing Computational Science Research Center, Beijing, China
| | - Rui-Qin Zhang
- Materials and Energy Division, Beijing Computational Science Research Center, Beijing, China
- Department of Physics, City University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
10
|
Ozawa M, Ozawa T, Nishio M, Ueda K. The role of CH/π interactions in the high affinity binding of streptavidin and biotin. J Mol Graph Model 2017; 75:117-124. [PMID: 28551501 DOI: 10.1016/j.jmgm.2017.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/27/2017] [Accepted: 05/02/2017] [Indexed: 11/28/2022]
Abstract
The streptavidin-biotin complex has an extraordinarily high affinity (Ka: 1015mol-1) and contains one of the strongest non-covalent interactions known. This strong interaction is widely used in biological tools, including for affinity tags, detection, and immobilization of proteins. Although hydrogen bond networks and hydrophobic interactions have been proposed to explain this high affinity, the reasons for it remain poorly understood. Inspired by the deceased affinity of biotin observed for point mutations of streptavidin at tryptophan residues, we hypothesized that a CH/π interaction may also contribute to the strong interaction between streptavidin and biotin. CH/π interactions were explored and analyzed at the biotin-binding site and at the interface of the subunits by the fragment molecular orbital method (FMO) and extended applications: PIEDA and FMO4. The results show that CH/π interactions are involved in the high affinity for biotin at the binding site of streptavidin. We further suggest that the involvement of CH/π interactions at the subunit interfaces and an extended CH/π network play more critical roles in determining the high affinity, rather than involvement at the binding site.
Collapse
Affiliation(s)
- Motoyasu Ozawa
- Central Research Laboratory, Kissei Pharmaceutical Co., Ltd., 4365-1 Hotakakashiwabara, Azumino, Nagano 399-8304, Japan.
| | - Tomonaga Ozawa
- Central Research Laboratory, Kissei Pharmaceutical Co., Ltd., 4365-1 Hotakakashiwabara, Azumino, Nagano 399-8304, Japan
| | | | - Kazuyoshi Ueda
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-Ku, Yokohama 240-8501, Japan
| |
Collapse
|
11
|
Driver RW, Claridge TDW, Scheiner S, Smith MD. Torsional and Electronic Factors Control the C-H⋅⋅⋅O Interaction. Chemistry 2016; 22:16513-16521. [PMID: 27709689 PMCID: PMC5113693 DOI: 10.1002/chem.201602905] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Indexed: 01/07/2023]
Abstract
The precise role of non‐conventional hydrogen bonds such as the C−H⋅⋅⋅O interaction in influencing the conformation of small molecules remains unresolved. Here we survey a series of β‐turn mimetics using X‐ray crystallography and NMR spectroscopy in conjunction with quantum calculation, and conclude that favourable torsional and electronic effects are important for the population of states with conformationally influential C−H⋅⋅⋅O interactions. Our results also highlight the challenge in attempting to deconvolute a myriad of interdependent noncovalent interactions in order to focus on the contribution of a single one. Within a small molecule that is designed to resemble the complexity of the environment within peptides and proteins, the interplay of different steric burdens, hydrogen‐acceptor/‐donor properties and rotational profiles illustrate why unambiguous conclusions based solely on NMR chemical shift data are extremely challenging to rationalize.
Collapse
Affiliation(s)
- Russell W Driver
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Timothy D W Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, 84322-0300, USA.
| | - Martin D Smith
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| |
Collapse
|
12
|
Gil A, Branchadell V, Calhorda MJ. A theoretical study of methylation and CH/π interactions in DNA intercalation: methylated 1,10-phenanthroline in adenine–thymine base pairs. RSC Adv 2016. [DOI: 10.1039/c6ra15495f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This work shows that quality is better that quantity to estabilize the intercalation of methylated phen.
Collapse
Affiliation(s)
- A. Gil
- Centro de Química e Bioquímica
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
| | - V. Branchadell
- Departament de Química
- Universitat Autònoma de Barcelona
- Barcelona
- Spain
| | - M. J. Calhorda
- Centro de Química e Bioquímica
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
| |
Collapse
|
13
|
Gil A, Melle-Franco M, Branchadell V, Calhorda MJ. How the Intercalation of Phenanthroline Affects the Structure, Energetics, and Bond Properties of DNA Base Pairs: Theoretical Study Applied to Adenine–Thymine and Guanine–Cytosine Tetramers. J Chem Theory Comput 2015; 11:2714-28. [DOI: 10.1021/ct5006104] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Adrià Gil
- Centro
de Química e Bioquímica, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | | | - Vicenç Branchadell
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Maria José Calhorda
- Centro
de Química e Bioquímica, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| |
Collapse
|
14
|
Nishio M, Umezawa Y, Fantini J, Weiss MS, Chakrabarti P. CH-π hydrogen bonds in biological macromolecules. Phys Chem Chem Phys 2015; 16:12648-83. [PMID: 24836323 DOI: 10.1039/c4cp00099d] [Citation(s) in RCA: 335] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.
Collapse
Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338, Minamioya, Machida-shi, Tokyo 194-0031, Japan.
| | | | | | | | | |
Collapse
|
15
|
Zhao C, Li P, Smith MD, Pellechia PJ, Shimizu KD. Experimental Study of the Cooperativity of CH−π Interactions. Org Lett 2014; 16:3520-3. [DOI: 10.1021/ol5014729] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Chen Zhao
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ping Li
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mark D. Smith
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Perry J. Pellechia
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ken D. Shimizu
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| |
Collapse
|
16
|
Zubatiuk TA, Shishkin OV, Gorb L, Hovorun DM, Leszczynski J. B-DNA characteristics are preserved in double stranded d(A)3·d(T)3 and d(G)3·d(C)3 mini-helixes: conclusions from DFT/M06-2X study. Phys Chem Chem Phys 2014; 15:18155-66. [PMID: 24065071 DOI: 10.1039/c3cp51584b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We report the results of the first comprehensive DFT study on the d(A)3·d(T)3 and d(G)3·d(C)3 nucleic acid duplexes. The ability of mini-helixes to preserve the conformation of B-DNA in the gas phase and under the influence of such factors as: solvent, uncompensated charge, and counter-ions was evaluated using M06-2X functional with 6-31G(d,p) basis set. The accuracy of the models was ascertained based on their ability to reproduce key structural features of natural B-DNA. Analysis of the helicity suggests that the helical conformations adopt geometrical parameters which are close to those of the B-DNA form. The torsion angles fall somewhere between the values observed for BI/BII conformational classes. The comparative analysis of parameters of isolated Watson-Crick base pairs versus B-DNA-like conformations indicates the same tendency of base-pair polarization and hydration. Specifically, effects of polarization of nucleobases in continuum type dielectric medium mimicking water are stronger than those caused by the presence of backbone. Polar environment as well as the presence of counterions stabilizes duplexes, facilitating helix formation. Substantial conformational changes of nucleotides upon duplex formation decrease the binding energy. In spite of structural and energetic changes, the placement of a mini-helix into the gas phase does not lead to significant disruption of the structure. On the contrary, the duplex preserves its helicity and the strands remain bound.
Collapse
Affiliation(s)
- Tetiana A Zubatiuk
- Division of Functional Materials Chemistry, SSI "Institute for Single Crystals" National Academy of Science of Ukraine, 60 Lenina Ave., Kharkiv, 61001, Ukraine
| | | | | | | | | |
Collapse
|
17
|
Atkinson A, Graton J, Le Questel JY. Insights into a highly conserved network of hydrogen bonds in the agonist binding site of nicotinic acetylcholine receptors: a structural and theoretical study. Proteins 2014; 82:2303-17. [PMID: 24752960 DOI: 10.1002/prot.24589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/02/2014] [Accepted: 04/15/2014] [Indexed: 11/07/2022]
Abstract
Structural and theoretical studies on the geometrical features of a hydrogen-bond network occurring in the binding site of nicotinic acetylcholine receptors (nAChRs) and composed of interconnected WxPD (Trp-x-Pro-Asp) and SWyz (Ser-Trp-yz) sequences from loops A and B, respectively, have been carried out. Multiple sequence alignments using as template the sequence of the apoform of Aplysia californica acetylcholine binding protein (Ac-AChBP) show the strict conservation of serine and tryptophan residues of the loop B SWyz sequence. Considering a sample of 19 high resolution AChBP structures, the strong conformational preferences of the key tryptophan residue has been pointing out, whatever the form, free or bounded, of AChBP. The geometry of the motif hydrogen-bond network has been characterized through the analyses of seven distances. The robustness of the various hydrogen-bond interactions is pointed out, the one involving the aspartate carboxylate group and the serine residue being the shortest of the network. The role of a cooperative effect involving a NH(His145)…OH (Ser142) hydrogen bond is highlighted. Density functional theory calculations on several simplified models based on the motif hydrogen-bond network allow probing the importance of the various hydrogen-bond interactions. The removal of the Ser142 hydroxyl group induces strong structural rearrangements, in agreement with the structural observations. Molecular electrostatic potential calculations on model systems highlight the importance of a cooperative effect in the whole hydrogen-bond network. More precisely, the key role of the Ser142 hydroxyl group, involved in several hydrogen bonds, is underlined.
Collapse
Affiliation(s)
- Alexandre Atkinson
- Université de Nantes, CEISAM UMR 6230, UFR des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, Nantes, F-44322, France
| | | | | |
Collapse
|
18
|
C-H…pi interactions in proteins: prevalence, pattern of occurrence, residue propensities, location, and contribution to protein stability. J Mol Model 2014; 20:2136. [DOI: 10.1007/s00894-014-2136-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 01/02/2014] [Indexed: 11/25/2022]
|
19
|
Alí-Torres J, Rimola A, Rodríguez-Rodríguez C, Rodríguez-Santiago L, Sodupe M. Insights on the Binding of Thioflavin Derivative Markers to Amyloid-Like Fibril Models from Quantum Chemical Calculations. J Phys Chem B 2013; 117:6674-80. [DOI: 10.1021/jp402807g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jorge Alí-Torres
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra
08193, Barcelona, Spain
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra
08193, Barcelona, Spain
| | - Cristina Rodríguez-Rodríguez
- Medicinal Inorganic Chemistry
Group, University of British Columbia,
2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Luis Rodríguez-Santiago
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra
08193, Barcelona, Spain
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra
08193, Barcelona, Spain
| |
Collapse
|
20
|
Pilar Carranza M, Manzano BR, Jalón FA, Rodríguez AM, Santos L, Moreno M. Experimental and theoretical evidence of unsupported Ag–Ag interactions in complexes with triazine-based ligands. Subtle effects of the symmetry of the triazine substituents. NEW J CHEM 2013. [DOI: 10.1039/c3nj00738c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
21
|
Galland N, Kone S, Le Questel JY. Mapping of the interaction sites of galanthamine: a quantitative analysis through pairwise potentials and quantum chemistry. J Comput Aided Mol Des 2012; 26:1111-26. [PMID: 22972560 DOI: 10.1007/s10822-012-9602-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 09/05/2012] [Indexed: 11/29/2022]
Abstract
A quantitative analysis of the interaction sites of the anti-Alzheimer drug galanthamine with molecular probes (water and benzene molecules) representative of its surroundings in the binding site of acetylcholinesterase (AChE) has been realized through pairwise potentials calculations and quantum chemistry. This strategy allows a full and accurate exploration of the galanthamine potential energy surface of interaction. Significantly different results are obtained according to the distances of approaches between the various molecular fragments and the conformation of the galanthamine N-methyl substituent. The geometry of the most relevant complexes has then been fully optimized through MPWB1K/6-31 + G(d,p) calculations, final energies being recomputed at the LMP2/aug-cc-pVTZ(-f) level of theory. Unexpectedly, galanthamine is found to interact mainly from its hydrogen-bond donor groups. Among those, CH groups in the vicinity of the ammonium group are prominent. The trends obtained provide rationales to the predilection of the equatorial orientation of the galanthamine N-methyl substituent for binding to AChE. The analysis of the interaction energies pointed out the independence between the various interaction sites and the rigid character of galanthamine. The comparison between the cluster calculations and the crystallographic observations in galanthamine-AChE co-crystals allows the validation of the theoretical methodology. In particular, the positions of several water molecules appearing as strongly conserved in galanthamine-AChE co-crystals are predicted by the calculations. Moreover, the experimental position and orientation of lateral chains of functionally important aminoacid residues are in close agreement with the ones predicted theoretically. Our study provides relevant information for a rational drug design of galanthamine based AChE inhibitors.
Collapse
Affiliation(s)
- Nicolas Galland
- UMR CNRS 6230, Chimie Et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UFR Sciences & Techniques, Université de Nantes, NANTES Cedex, France
| | | | | |
Collapse
|
22
|
Kang YK, Byun BJ. Strength of CH···π interactions in the C-terminal subdomain of villin headpiece. Biopolymers 2012; 97:778-88. [DOI: 10.1002/bip.22062] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
23
|
Chung MK, White PS, Lee SJ, Waters ML, Gagné MR. Self-Assembled Multi-Component Catenanes: Structural Insights into an Adaptable Class of Molecular Receptors and [2]-Catenanes. J Am Chem Soc 2012; 134:11415-29. [DOI: 10.1021/ja302345n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Mee-Kyung Chung
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
| | - Peter S. White
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
| | - Stephen J. Lee
- U.S. Army Research Office, P.O.
Box 12211, Research Triangle Park, North Carolina 27709, United States
| | - Marcey L. Waters
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
| | - Michel R. Gagné
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
| |
Collapse
|
24
|
Chung MK, Lee SJ, Waters ML, Gagné MR. Self-Assembled Multi-Component Catenanes: The Effect of Multivalency and Cooperativity on Structure and Stability. J Am Chem Soc 2012; 134:11430-43. [DOI: 10.1021/ja302347q] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mee-Kyung Chung
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
| | - Stephen J. Lee
- U.S. Army Research Office, P.O. Box 12211, Research Triangle Park, North
Carolina 27709, United States
| | - Marcey L. Waters
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
| | - Michel R. Gagné
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
| |
Collapse
|
25
|
|
26
|
He G, Kwok CK, Lam SL. Preferential base pairing modes of T·T mismatches. FEBS Lett 2011; 585:3953-8. [PMID: 22101148 DOI: 10.1016/j.febslet.2011.10.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/06/2011] [Accepted: 10/26/2011] [Indexed: 10/15/2022]
Abstract
It has long been recognized that T·T mismatches can adopt two different modes of exchangeable wobble base pairs in which no preferential pairing mode has been observed. In this study, we have performed a systematic nuclear magnetic resonance (NMR) investigation to study the sequence context effect on the pairing modes of T·T mismatches. Our results reveal for the first time that preferential pairing mode does exist in T·T mismatches with specific type of flanking base pairs.
Collapse
Affiliation(s)
- Guoyun He
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | | | | |
Collapse
|
27
|
Ozawa T, Okazaki K, Kitaura K. CH/π hydrogen bonds play a role in ligand recognition and equilibrium between active and inactive states of the β2 adrenergic receptor: An ab initio fragment molecular orbital (FMO) study. Bioorg Med Chem 2011; 19:5231-7. [DOI: 10.1016/j.bmc.2011.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/01/2011] [Accepted: 07/02/2011] [Indexed: 10/17/2022]
|
28
|
Churchill CDM, Wetmore SD. Developing a computational model that accurately reproduces the structural features of a dinucleoside monophosphate unit within B-DNA. Phys Chem Chem Phys 2011; 13:16373-83. [PMID: 21842033 DOI: 10.1039/c1cp21689a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ability of a dinucleoside monophosphate to mimic the conformation of B-DNA was tested using a combination of different phosphate models (anionic, neutral, counterion), environments (gas, water), and density functionals (B3LYP, MPWB1K, M06-2X) with the 6-31G(d,p) basis set. Three sequences (5'-GX(Py)-3', where X(Py) = T, U or (Br)U) were considered, which vary in the (natural or modified) 3' pyrimidine nucleobase (X(Py)). These bases were selected due to their presence in natural DNA, structural similarity to T and/or applications in radical-initiated anti-tumour therapies. The accuracy of each of the 54 model, method and sequence combinations was judged based on the ability to reproduce key structural features of natural B-DNA, including the stacked base-base orientation and important backbone torsion angles. B3LYP yields distorted or tilted relative base-base orientations, while many computational challenges were encountered for MPWB1K. Despite wide use in computational studies of DNA, the neutral (protonated) phosphate model could not consistently predict a stacked arrangement for all sequences. In contrast, stacked base-base arrangements were obtained for all sequences with M06-2X in conjunction with both the anionic and (sodium) counterion phosphate models. However, comparison of calculated and experimental backbone conformations reveals the charge-neutralized counterion phosphate model best mimics B-DNA. Structures optimized with implicit solvent (water) are comparable to gas-phase structures, which suggests similar results should be obtained in an environment of intermediate polarity. We recommend the use of either gas-phase or water M06-2X optimizations with the counterion phosphate model to study the structure and/or reactivity of natural or modified DNA with a dinucleoside monophosphate.
Collapse
Affiliation(s)
- Cassandra D M Churchill
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | | |
Collapse
|
29
|
Ozawa T, Okazaki K, Kitaura K. Importance of CH/π hydrogen bonds in recognition of the core motif in proline-recognition domains: an ab initio fragment molecular orbital study. J Comput Chem 2011; 32:2774-82. [PMID: 21710635 DOI: 10.1002/jcc.21857] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 05/11/2011] [Accepted: 05/13/2011] [Indexed: 11/07/2022]
Abstract
We examined CH/π hydrogen bonds in protein/ligand complexes involving at least one proline residue using the ab initio fragment molecular orbital (FMO) method and the program CHPI. FMO calculations were carried out at the Hartree-Fock (HF)/6-31G*, HF/6-31G**, second-order Møller-Plesset perturbation (MP2)/6-31G*, and MP2/6-31G** levels for three Src homology 3 (SH3) domains and five proline-recognition domains (PRDs) complexed with their corresponding ligand peptides. PRDs use a conserved set of aromatic residues to recognize proline-rich sequences of specific ligands. Many CH/π hydrogen bonds were identified in these complexes. CH/π hydrogen bonds occurred, in particular, in the central part of the proline-rich motifs. Our results suggest that CH/π hydrogen bonds are important in the recognition of SH3 and PRDs by their ligand peptides and play a vital role in the signal transduction system. Combined use of the FMO method and CHPI analysis is a valuable tool for the study of protein/protein and protein/ligand interactions and may be useful in rational drug design.
Collapse
Affiliation(s)
- Tomonaga Ozawa
- Central Research Laboratory, Kissei Pharmaceutical Company Ltd, Azumino-city, Nagano, 399-8304, Japan.
| | | | | |
Collapse
|
30
|
Liu H, Mu J, Lee JY. Charge Transport Properties of Stacking Bisindenoanthrazolines: DFT Studies. J Phys Chem B 2011; 115:8409-16. [DOI: 10.1021/jp202745w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hongguang Liu
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Jinglin Mu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
- Supercomputing Center, Korea Institute of Science and Technology Information, Yuseong, Daejeon 305-806, Korea
| |
Collapse
|
31
|
Nishio M. The CH/π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates. Phys Chem Chem Phys 2011; 13:13873-900. [PMID: 21611676 DOI: 10.1039/c1cp20404a] [Citation(s) in RCA: 624] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CH/π hydrogen bond is an attractive molecular force occurring between a soft acid and a soft base. Contribution from the dispersion energy is important in typical cases where aliphatic or aromatic CH groups are involved. Coulombic energy is of minor importance as compared to the other weak hydrogen bonds. The hydrogen bond nature of this force, however, has been confirmed by AIM analyses. The dual characteristic of the CH/π hydrogen bond is the basis for ubiquitous existence of this force in various fields of chemistry. A salient feature is that the CH/π hydrogen bond works cooperatively. Another significant point is that it works in nonpolar as well as polar, protic solvents such as water. The interaction energy depends on the nature of the molecular fragments, CH as well as π-groups: the stronger the proton donating ability of the CH group, the larger the stabilizing effect. This Perspective focuses on the consequence of this molecular force in the conformation of organic compounds and supramolecular chemistry. Implication of the CH/π hydrogen bond extends to the specificity of molecular recognition or selectivity in organic reactions, polymer science, surface phenomena and interactions involving proteins. Many problems, unsettled to date, will become clearer in the light of the CH/π paradigm.
Collapse
Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338 Minamioya, Machida-shi, Tokyo, 194-0031, Japan.
| |
Collapse
|
32
|
Niu Z, Slebodnick C, Bonrad K, Huang F, Gibson HW. The First [2]Pseudorotaxane and the First Pseudocryptand-Type Poly[2]pseudorotaxane Based on Bis(meta-phenylene)-32-Crown-10 and Paraquat Derivatives. Org Lett 2011; 13:2872-5. [DOI: 10.1021/ol200862b] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhenbin Niu
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Carla Slebodnick
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Klaus Bonrad
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Feihe Huang
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Harry W. Gibson
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| |
Collapse
|
33
|
Takahashi O, Kohno Y, Nishio M. Relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates: evidence from recent experimental data and high-level ab initio MO calculations. Chem Rev 2011; 110:6049-76. [PMID: 20550180 DOI: 10.1021/cr100072x] [Citation(s) in RCA: 447] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osamu Takahashi
- Department of Chemistry, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan.
| | | | | |
Collapse
|
34
|
Fujii A, Hayashi H, Park JW, Kazama T, Mikami N, Tsuzuki S. Experimental and theoretical determination of the accurate CH/π interaction energies in benzene–alkane clusters: correlation between interaction energy and polarizability. Phys Chem Chem Phys 2011; 13:14131-41. [DOI: 10.1039/c1cp20203k] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
35
|
Acosta-Silva C, Branchadell V, Bertran J, Oliva A. Mutual relationship between stacking and hydrogen bonding in DNA. Theoretical study of guanine-cytosine, guanine-5-methylcytosine, and their dimers. J Phys Chem B 2010; 114:10217-27. [PMID: 20684646 DOI: 10.1021/jp103850h] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The mutual relationship between stacking and hydrogen-bonding and the possible influence of stacking in the different behavior of cytosine (C) and 5-methylcytosine (C') in DNA have been studied through complete DFT optimization of different structures of G-C and G-C' dimers (i.e., G-C/C-G and G-C'/C'-G), using four different functionals. Our results show that stacking leads to an increase of the O(6)...H-N(4) hydrogen bond length and to a simultaneous decrease of the N(2)-H...O(2) one, in such a way that both lengths approach each other and, in some cases, an inversion occurs. These results suggest that stacking can be a factor to explain the disparity between theory and experiment on the relative strength of the two lateral hydrogen bonds. Regarding the difference between cytosine and 5-methylcytosine, we have shown that methylation enhances the stacking interactions, mainly due to the increase of polarizability. Methylation also favors the existence of slid structures which can produce local distortions of DNA.
Collapse
Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193 Spain
| | | | | | | |
Collapse
|
36
|
Liu H, Kang S, Lee JY. Electronic Structures and Charge Transport of Stacked Annelated β-Trithiophenes. J Phys Chem B 2010; 115:5113-20. [DOI: 10.1021/jp1045595] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hongguang Liu
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Sunwoo Kang
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| |
Collapse
|
37
|
Nayak SK, Sathishkumar R, Row TNG. Directing role of functional groups in selective generation of C–H⋯π interactions: In situ cryo-crystallographic studies on benzyl derivatives. CrystEngComm 2010. [DOI: 10.1039/c001190h] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
38
|
Churchill CDM, Navarro-Whyte L, Rutledge LR, Wetmore SD. Effects of the biological backbone on DNA-protein stacking interactions. Phys Chem Chem Phys 2009; 11:10657-70. [PMID: 20145810 DOI: 10.1039/b910747a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The pi-pi stacking (face-to-face) interactions between the five natural DNA or RNA nucleobases and the four aromatic amino acids were compared using three different types of dimers: (1) a truncated nucleoside (nucleobase) stacked with a truncated amino acid; (2) a truncated nucleoside (nucleobase) stacked with an extended amino acid; and (3) a nucleoside (extended nucleobase) stacked with a truncated amino acid. Systematic (MP2/6-31G*(0.25)) potential energy surface scans reveal important information about the effects of the deoxyribose sugar and protein backbone on the structure and binding energy between truncated nucleobase and amino acid models that are typically implemented in the literature. Most notably, electrostatic and steric interactions arising from the bulkiness of the biological backbones can change the preferred relative orientations of DNA and protein pi-systems. More importantly, the protein backbone can strengthen the stacking energy (by up to 10 kJ mol(-1)), while the deoxyribose moiety can strengthen or weaken the stacking interaction depending on the positioning of the amino acid relative to the sugar residue. These effects are likely due to additional interactions between the amino acid or nucleobase ring and the backbone in the extended monomer rather than significant changes in the properties of the biological pi-systems upon model extension. Since the present work reveals that all calculated DNA-protein stacking interactions are significant and approach the strength of other noncovalent interactions between biomolecules, both pi-pi and backbone-pi interactions must be considered when attempting to gain a complete picture of DNA-protein binding.
Collapse
Affiliation(s)
- Cassandra D M Churchill
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | | | | | | |
Collapse
|
39
|
Gil A, Branchadell V, Bertran J, Oliva A. An analysis of the different behavior of DNA and RNA through the study of the mutual relationship between stacking and hydrogen bonding. J Phys Chem B 2009; 113:4907-14. [PMID: 19284733 DOI: 10.1021/jp809737c] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The mutual relationship between stacking and hydrogen bonding and the possible influence of stacking in the different behavior of DNA and RNA base pairs have been studied through complete DFT optimization of different structures of A-U and A-T dimers (i.e., A-U/U-A and A-T/T-A), using some functionals developed by the group of Truhlar. The results obtained in this work clearly show that stacking and hydrogen bonding are deeply connected. The different behavior of DNA and RNA when replacing uracil by thymine can be interpreted through the formation of a stabilizing CH/pi interaction between the methyl group of thymine and the five-member ring of adenine.
Collapse
Affiliation(s)
- Adrià Gil
- Departament de Quimica, Universitat Autonoma de Barcelona, Bellaterra 08193, Spain
| | | | | | | |
Collapse
|
40
|
Rutledge LR, Durst HF, Wetmore SD. Evidence for Stabilization of DNA/RNA−Protein Complexes Arising from Nucleobase−Amino Acid Stacking and T-Shaped Interactions. J Chem Theory Comput 2009; 5:1400-10. [DOI: 10.1021/ct800567q] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Holly F. Durst
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| |
Collapse
|
41
|
Sherrill CD. Computations of Noncovalent π Interactions. REVIEWS IN COMPUTATIONAL CHEMISTRY 2009. [DOI: 10.1002/9780470399545.ch1] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
|
42
|
Maity S, Sedlak R, Hobza P, Patwari GN. Infrared–optical double resonance spectroscopic measurements and high level ab initio calculations on a binary complex between phenylacetylene and borane-trimethylamine. Understanding the role of C–H⋯π interactions. Phys Chem Chem Phys 2009; 11:9738-43. [DOI: 10.1039/b911926d] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
43
|
Nishio M, Umezawa Y, Honda K, Tsuboyama S, Suezawa H. CH/π hydrogen bonds in organic and organometallic chemistry. CrystEngComm 2009. [DOI: 10.1039/b902318f] [Citation(s) in RCA: 481] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
44
|
Lait LA, Rutledge LR, Millen AL, Wetmore SD. yDNA versus xDNA Pyrimidine Nucleobases: Computational Evidence for Dependence of Duplex Stability on Spacer Location. J Phys Chem B 2008; 112:12526-36. [DOI: 10.1021/jp805547p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Linda A. Lait
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
| | - Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
| | - Andrea L. Millen
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
| |
Collapse
|
45
|
Rutledge LR, Wetmore SD. Remarkably Strong T-Shaped Interactions between Aromatic Amino Acids and Adenine: Their Increase upon Nucleobase Methylation and a Comparison to Stacking. J Chem Theory Comput 2008; 4:1768-80. [DOI: 10.1021/ct8002332] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| |
Collapse
|
46
|
Moitessier N, Englebienne P, Lee D, Lawandi J, Corbeil CR. Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br J Pharmacol 2008; 153 Suppl 1:S7-26. [PMID: 18037925 PMCID: PMC2268060 DOI: 10.1038/sj.bjp.0707515] [Citation(s) in RCA: 316] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 09/18/2007] [Accepted: 09/24/2007] [Indexed: 11/08/2022] Open
Abstract
Accelerating the drug discovery process requires predictive computational protocols capable of reducing or simplifying the synthetic and/or combinatorial challenge. Docking-based virtual screening methods have been developed and successfully applied to a number of pharmaceutical targets. In this review, we first present the current status of docking and scoring methods, with exhaustive lists of these. We next discuss reported comparative studies, outlining criteria for their interpretation. In the final section, we describe some of the remaining developments that would potentially lead to a universally applicable docking/scoring method.
Collapse
Affiliation(s)
- N Moitessier
- Department of Chemistry, McGill University, Montréal, Québec, Canada.
| | | | | | | | | |
Collapse
|
47
|
Kumar J, Purohit CS, Verma S. Directing spatial disposition of ferrocene around homoadenine tetrads. Chem Commun (Camb) 2008:2526-8. [DOI: 10.1039/b802051e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
48
|
Mondal P, Karmakar A, Singh WM, Baruah JB. Crystal packing in some flexible carboxylic acids and esters attached to a naphthalene ring. CrystEngComm 2008. [DOI: 10.1039/b808399a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
49
|
Tsuzuki S, Fujii A. Nature and physical origin of CH/π interaction: significant difference from conventional hydrogen bonds. Phys Chem Chem Phys 2008; 10:2584-94. [DOI: 10.1039/b718656h] [Citation(s) in RCA: 288] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|